Guns in the Valley
by Ragnarooke
Summary: After discovering what he really is and preventing Third Impact, Shinji Ikari sets out to find his place in the world. Along the way, he'll meet new friends, new enemies and legends from times past. Will he learn how to truly be a hero and protect his loved ones?


Chapter 1: Awakening

Evangelion belongs to Gainax. Logan belongs to Marvel and Fox. I don't own anything, so please don't sue me.

 **XXXXXX**

Doctor Ritsuko Akagi, head scientist of NERV yawned to herself while surveying the retrieval of Evangelion Unit-01. It had only been a few hours since the miraculous defeat of the Third Angel by the berserk war machine. Its pilot, 14-year-old Shinji Ikari had been unconscious for most of the grueling encounter. He had tried desperately to fight but the neural feedback had swiftly knocked him out once he started losing.

His abnormally high synch rate didn't exactly help his chances. Ritsuko found it odd someone who had never even seen an Eva could achieve a synch rate of 40%. It was physically impossible, or so she thought.

' _I'll have to look into this.'_ Ritsuko thought to herself.

A small portion of the doctor's mind felt sorry for the boy. Seeing your estranged father after not having seen the man for a decade and being guilt tripped into piloting said father's weapon of war wasn't exactly the best family reunion. Ritsuko quickly banished those thoughts. The pilots were merely tools to the commander and Seele, Rei was proof of that.

Plus she had an image to obtain.

It was then that her phone rang. It was a call from the nursing staff in NERV's medical wing. The nurse informed the good doctor that Tokyo-3's savior was now awake.

Ritsuko hummed in acknowledgement. "Thank you for informing me. I'll have someone see to him shortly." Ritsuko said to the nurse.

"One last thing Dr. Akagi. We did all the tests for angel contamination like you ordered and well, we found something unusual about the Third Child's skeletal structure." The nurse replied.

"What is it?" Ritsuko asked.

"That's just it ma'am, we aren't sure. We've confirmed it isn't contamination but we're still unsure of what it is. Dr. Yamagishi thinks it's some sort of deformity caused by the radiation from the Second Impact." The nurse replied unsurely.

"Alright, forward it to my computer and I'll have a look." Ritsuko ordered.

"Yes ma'am!" The nurse barked.

And with that the call was ended. Ritsuko turned to her left and informed her friend Captain Misato Katsuragi that Shinji was now awake in the medical ward. She and Misato exchanged a few minutes of small talk before the Captain set off to check Shinji out of the hospital and Ritsuko continued her job of overseeing the retrieval of Unit-01.

 **XXXXXX**

It was not until late that night that Ritsuko got a chance to check the details sent to her computer. She had quite the busy day, what with being in charge of the retrieval operation and looking for samples of the Third Angel that weren't contaminated.

She had no luck with the samples but luckily the cleanup and retrieval went without problems.

Ritsuko yawned heavily before switching on the coffee maker in her office. It had been almost 24 hours since she had last slept and she just wanted to do a quick check on the information of the Third Child's bones before finally going home and getting some sleep.

The good doctor lazily logged into her terminal before finding the file sent to her from the nursing staff. When she opened the file, all notions of sleep left Ritsuko's mind. The photo of the boy's skeleton taken via x-ray left the doctor stunned.

' _What the hell is that!?'_ Ritsuko thought to herself.

It took her all of three seconds to realise what she was looking at, or at least what she thought it was. She had thought it impossible, they were supposed to be extinct! It couldn't just be a deformity. It looked so similar to what HE could do.

' _The commanders and Seele cannot find out about this.'_ Ritsuko thought heavily.

She was undoubtedly loyal to Commander Ikari, but his son was now what Ritsuko hesitated to call a miracle of nature. She had been around long enough to witness their fall. Ironically, it was them that gave humanity a common goal right before Second Impact. The one thing that puzzled her is how similar Shinji's gift was to HIS.

"I'll have to perform some tests." Ritsuko said aloud.

She then downloaded all the information on the file onto her flash drive before deleting any trace the file had existed on her computer. In retrospect Ritsuko thought the last 24 hours had been quite good in hindsight. The Third Angel had been defeated and one of nature's great mysteries had been dropped into her lap.

Assuming Shinji decided to stay in the city.

With a smile on her face Ritsuko stood up, poured herself a cup of coffee, and switched off the coffee maker along with the lights.

' _Now it's time for some much needed rest.'_ She thought.

She made to swing by NERV's hospital to inform the staff that had checked on Shinji not to mention their findings on the Third Child under any circumstances.

 **XXXXXX**

 **Timeskip: 2 days after the defeat of the Fifth Angel**

Shinji awoke with a start to the sound of his alarm clock blaring its annoying ring from the desk it sat on. Shinji stretched his arms and got up from his bed. He reached to turn the alarm off, careful not to hurt his hands. After Shinji had killed the angel, he had burned his hands on his fellow pilot Rei Ayanami's entry plug in an attempt to get her out of the cylindrical coffin.

His plugsuit had absorbed some of the searing heat but swiftly melted away, leaving the Third Child with 3rd degree burns on both hands. Doctor Akagi had given the boy some ointment to treat the burns along with some bandages she had told him to change daily.

As Shinji hit the button to silence the alarm he noticed the familiar pain he received whenever he touched something with his hands the day before was gone.

"What the heck?" He whispered to himself.

Shinji then hurriedly but carefully removed the bandages on his hands. What he saw made his jaw drop. The Third Child stared in shock at his hands. The burns that had previously occupied his palms and fingers were no more. It was as if they had healed by some sort of magic or something.

"Impossible…" Shinji breathed.

Shinji didn't know what to make of the newly healed appendages. Just hours ago his hands were scarred and very painful. Now they were fine, no traces that he had even gotten the injuries were present.

Shinji knew he'd have to talk to Doctor Akagi about this. The ointment she gave him couldn't possibly do something like this, could it? He wouldn't know until he got a chance to talk with her. Luckily for him, he wouldn't have to wait long.

He and Rei had a synch test later that afternoon.

Shinji decided that school just wasn't an option that day and quickly put on some fresh bandages in order to keep his newly healed hands a secret. He wasn't particularly worried about Misato finding out, but her protective nature and teasing personality could leave Shinji quite frazzled sometimes. His friends Touji and Kensuke were a whole other story. They would demand answers. Answers Shinji didn't have.

And stress about how his wounds miraculously healed was not something the boy needed at the moment. He had just killed another angel only two days ago.

He decided that he would tell Misato that his hands still hurt too bad to write. Shinji knew she would believe him. Misato had no reason not to.

With his goal set Shinji grabbed his pink shirt and blue jeans from his closet before heading to the bathroom for a quick shower. As he walked down the hallway towards the bathroom Shinji noticed something that stopped him in his tracks.

He smelled something.

It was something he'd never smelled before, not necessarily bad but certainly unique. ' _It smells like beer, fish, and something else all mixed together.'_ Shinji wondered. He continued down the hallway, following the scent.

When he reached the kitchen he found the source of the odd smell. It was coming from Pen-Pen's fridge! As Shinji approached the fridge its inhabitant made himself known by opening the tiny sliding door and giving the boy a good morning "Wark" before heading into the living room to watch the morning news.

As Pen-Pen left, so did the odd smell.

That left the pilot of Unit-01 completely puzzled. He had no idea why Pen-Pen smelled so weird this morning, considering the bird took baths regularly. The odd scent permeating from the penguin was still present but not nearly as strong as when he was in the same room as the boy.

It was almost as if the warm water fowl left a trail of whatever was radiating from him.

The slam of a door and the sound of loud yawning signaled Shinji that his guardian was now awake. As her shuffling footfalls got closer to the kitchen Shinji turned to greet her a good morning. Ever since Shinji had moved into her apartment Misato had proven herself to be a good, albeit sloppy guardian. All in all, he was glad he lived there with the voluptuous captain.

She rounded the corner, responded to Shinji's greeting with a half hearted wave and made a beeline for the other fridge in the room. Shinji couldn't help but smile and roll his eyes as she took a beer out of the fridge, popped the top and proceeded to down the entire can in one go.

"Yeehaw! Good mornin' Shin-chan!" Misato yelled.

"Good morning, Misato-san." He responded.

Shinji then noticed another strange scent, coming from Misato this time. It was a mixture of beer and lavender perfume. Again like with Pen-Pen, the scent followed her as she moved towards him.

"How are your hands today, kiddo?" She asked him.

"Not as bad as yesterday, but they still hurt pretty bad. Can I stay home today?" He answered with a question.

"Of course Shinji, but remember you still have a synch test at 5 today." Misato agreed.

"I know. I'll be there in time." Shinji added.

"I have to go into NERV today. Do you want me to come pick you up before the test?" She asked.

"No, I'll walk today. A little fresh air would be nice." Shinji commented.

And with that the two roommates officially began their morning. Misato had let him shower first, and unknown to him decided to do her charge a favor and cook breakfast while he showered. When she had told him that she had cooked breakfast while he was busy Shinji had prepared for the worst.

Luckily for him she chose pancakes. It was one of the few things she could cook well.

After the two flatmates ate, Misato began to get ready for work. After she had gotten ready Shinji met her at the the door to see her off and give her the lunch he made for her. "Shinji, you didn't have to do that. Especially not with your hands in the state they're in!" She announced.

"It's alright, I don't mind Misato-san." Shinji claimed.

"It's not that I don't appreciate it Shinji, but don't worry yourself with trivial things like making lunch for an old lady like me with your hands in their current state!" Misato ordered.

"Yes ma'am." He whispered.

"But I'm glad you made it. Thank you Shin-chan." She cooed and gave the boy one of her patented Misato-sized bear hugs. She then tickled the boy furiously to wipe the sad expression from his face. Their laughter filled the apartment forcing Pen-Pen to turn up the volume on the TV.

"Alright, I'm off to work. If anything happens, call me. I'll see you at NERV." Misato announced as she stopped tickling him.

"Ok, see you then!" Shinji laughed.

With that Misato slipped on her shoes, accepted the lunch from Shinji's bandaged hands and opened the door to leave. When she did a small breeze brought with it another strange odor. He only smelled it for a brief second before the door closed once more, but it was undoubtly there.

"What is going on?" Shinji questioned to himself.

A "Wark" from behind him was all the response he got. Normally Pen-Pen sneaking up on him scared the boy, but the penguin hadn't gotten the drop on him this morning. Shinji had actually smelled the bird before he announced his presence.

"This is too weird. What am I part dog now or something?" Shinji breathed.

The lightbulb inside Shinji's mind suddenly switched on. He reasoned if his sense of smell really had been enhanced somehow, a little trip outside would be the easiest way to find out. But he couldn't stay out for long because of Section-2.

The black suited security force had orders to watch him every time he left the apartment, but unfortunately for them they were all too easy for him to give them the slip. Safe to say a long morning stroll while ditching his assigned security force right after he had asked Misato to stay home because his hands still hurt wouldn't look good on his record. He'd get chewed out for sure.

He scratched his head before grinning as a convenient excuse came to his mind.

It was his turn to take the garbage to the dumpster. Usually he did it when he left for school but with his current predicament he forgot, until now. Shinji then ran into the kitchen and tied up the garbage bag inside the trash can before rushing back to front door, putting on his shoes, picking up the trash bag again, and opening the front door.

When Shinji stepped outside onto the open hallway of the apartment building, it was like he was seeing the world for the first time.

He could smell a million things at once. Some smells familiar, others new, but all were unique. Shinji recognized food being cooked from the small restaurant two blocks away, exhaust from the cars in the street, and fresh cut grass in the distance.

The mental reminder that Section-2 was always watching snapped Shinji out of his trance. He closed the front door and made his way to the elevator that lead to the apartment building's lobby.

After 30 seconds of annoying elevator music Shinji reached the lobby. He then exited the elevator and headed to the front door, waving to the woman behind the front desk who responded with a wave of her own.

When Shinji exited the lobby he felt like his sense of smell had gone into maximum overdrive. Everything all melded together, making him unable to tell any of the scents apart. It was beginning to give him a headache, and a very slight pain had begun to form in his hands and forearms.

Shinji then wanted nothing more than to return to the safety of the apartment where smells didn't give him a headache so he hurried and placed the trash into the dumpster before returning to his Fortress of Solitude for the day.

When he returned Shinji placed a new trash bag into the can and glanced at the clock. "Hm, it's only 8:30, looks like today's gonna be one of those days." He mused.

With the thought of the long, boring day ahead, the Third Child grabbed his smartphone, walkman, and a book from his room. He then sat down next to Pen-Pen in the living room. As the warm water penguin lay glued to the TV, Shinji opened his book and started reading. Unlike other kids his age Shinji barely used his phone, preferring literature to social media and the internet.

Hell, before he moved to Tokyo-3 Shinji hadn't even owned a phone. His teacher said they were an unnecessary distraction. Misato had gotten his phone for him. He had tried to sway her otherwise and not waste her money on him but she had insisted. "NERV needs a way to contact you when a new angel shows up or if there's an emergency. Besides, how else are the ladies gonna get in touch with ya without a phone Shin-chan!" She had said.

He smiled at the memory. Misato could tease him up a storm and was a strict commanding officer, but in the end Shinji was glad to have the purple haired beauty around. She was the only person Shinji felt truly cared about him. He also new that he was a tool to her. She needed him to pilot the Eva, but he still felt like her care was genuine.

That fact alone made looking in the mirror each morning a little easier on the depressed lad.

A small spike of increased pain that flowed from his forearms into his hands wiped all thought of his self image and his guardian from his mind. Shinji yelped at the sudden pain. The slight pain that had formed while he was taking out the trash had increased slightly from the small spike.

' _Now what?'_ He wondered.

Shinji didn't have to wait too long before he got an answer.

Over the course of only a couple of hours, the slight pain had increased to a dull throbbing and recently, unbearable agony. The boy felt as if his arms might explode. And if that wasn't bad enough the mental images started.

Still images of the boy's life flashed before his eyes, all going a million miles an hour. Every bad part of his life was suddenly thrown back into his face.

The nasty combination of physical and mental pain had reduced him to a whimpering pile of flesh. Tears streamed down his face and he couldn't suppress a howl of pain as the burning in his hands and forearms increased to levels of pain that rivaled what he felt when being boiled alive by the Fifth Angel.

He wanted to scream, wanted for someone to help him but the images and the intense burning seemed to take all motor control from his brain. He reached desperately for his phone but it wasn't where he had lain it earlier due to his scream having scared Pen-Pen. The frightened bird had accidently knocked the cellphone from its place next to the boy on the floor when he made his frantic exit.

The images began to fade enough for him to be able to see through them and his tears. Within a few seconds they faded completely. The burning pain also disappeared right after. It was then that Shinji noticed where Pen-Pen had knocked his phone to. He had to call Misato, he wouldn't make it to even see Doctor Akagi at this rate.

He regretted not calling her when the pain was just tolerable. He understood now that something was very wrong with him. No simple ointment given to him could heal third degree burns and make him feel like he was about to die.

Shinji leapt from his position on the floor and rushed over to his smartphone before rapidly punching in Misato's number. Unfortunately for him, he never got finish typing in the first the three digits before the unholy pain returned with a vengeance. Shinji's phone fell from his hands and clattered to the floor. The Third Child followed suit and collapsed to his knees. The burning was so intense this time Shinji saw spots.

And unlike before, this time Shinji did scream. A lot, and very loudly.

In his insane howling, Shinji didn't notice the objects moving under the skin of his knuckles until it happened. In one violent motion Shinji let out one last guttural scream that was more akin to a roar as six, 10-inch bone claws erupted from between the boy's knuckles. Three on each hand.

Shinji had stopped screaming and could only stare at the bony protrusions with a look of horror painted on his face. Blood trickled down from the wounds the claws had made and dripped onto the hardwood floor.

It took a full 5 minutes before Shinji could snap himself out of his trance-like staring. He moved his hands with such care you'd think he was cradling a newborn baby. Shinji realised he could still move his fingers with some difficulty. But the boy found it much easier just to clench his hands into fists.

"What the fuck's wrong with me!" He whispered in terror.

Shinji was about to try and call Misato again when he moved his arms and felt a sensation unlike he had ever felt before. It was like he was moving muscles he didn't know he had. Shinji focused on the feeling.

What happened next shocked the horrified lad even more.

When Shinji focused on the sensation, the three bone claws on each hand slowly retracted back into his knuckles and into his forearms. The wounds where the claws had exited quickly healed and the only trace of the whole event had took place was the blood that stained Shinji's hands and the floor, along with his rugged breathing. It didn't hurt when the claws retracted but Shinji still felt like vomiting.

Shinji took a moment to compose himself, before he screamed once more.

"WHAT THE FUCK'S GOING ON!?" Shinji bellowed.

There was no response.

Pen-Pen had merely peeked around the corner to the living room, shaking in fear. Not any response from neighbors either. That was because they had no neighbors. The building was owned by NERV, serving as an officer's housing building. But since the building lie towards the outermost part of the city, no one wanted to live there on account of how long it took to get to work.

But with the way Misato drove, she could easily make up for lost time.

Speaking of time, when Shinji went to call Misato he noticed the time read 4:15. The synch test started at 5. He decided then that he wouldn't call Misato unless it was absolutely necessary, he could make it on his own. The pain was gone now, but new feeling was still there. He focused on it once more with violent results.

The three claws on each arm broke easily through the skin of his knuckles once again. It hurt far less this time, but it was still enough to make him yelp. The wounds also bled far less this go around. After a few seconds of messing around with the feeling Shinji found he could pop and retract his claws at will, each time faster and less painful than the last. The wounds the claws made stopped bleeding as well.

"Just like Wolverine, but without metal!" Shinji marveled.

His homeroom teacher often droned on about the X-Men when not talking about Second Impact, so the adamantium berserker had left quite the impression in the young pilot's mind. Not so much for Touji and Kensuke, as those two had heard it all far more than Shinji had. They had been stuck with the old coot as their homeroom teacher for two years.

But he knew he wasn't anything special like Wolverine. He figured this dilemma was the result of the angelic contamination everyone at NERV always spoke of.

After the shock and fear wore off, Shinji realised if he didn't get to NERV he'd be late for the test. And what better way to find out what was wrong with him than the place that made the impossible, possible.

Shinji stood from his spot on the floor and rushed to the kitchen where he washed the blood from his hands and arms before grabbing some paper towels and cleaner to take care of the small puddle of blood on the living room floor.

He snatched his phone from the floor, ran to his room to grab his wallet which contained his NERV card, ran back to the front door to put his shoes on, before locking the door and sprinting to his destination.

If he wasn't fast he would miss the train that stopped next to the NERV checkpoint that he normally used to get into the Geofront. For the sake of politeness he walked through the building's lobby but increased his pace to a full sprint once he was outside.

It had taken him only five minutes to arrive at the train station where it usually took him fifteen. He had run over two miles and here he stood, barely breaking a sweat. In his haste Shinji remembered that his claws had burst through his bandages and soaked them in blood. Shinji had thrown the bloody bandages away but was cursing himself for not putting on fresh ones.

If someone he knew saw his hands that were supposed to be burned, they'd know something was up. So as he boarded the train to the checkpoint he decided he'd just keep his hands out of sight.

It took only a few minutes before the train arrived at its destination allowing Shinji off and he walked over to the checkpoint before pulling out his NERV card and swiping it through the security clearance gate. The card terminal pinged green and the large door in front of him opened with a familiar hiss of air.

He put his card away, stuffed his hands into his pockets, and continued towards NERV headquarters. He took a second train that took him to bottom of the Geofront where the pyramid shaped headquarters lay and exited into the maze-like halls of NERV. As the boy continued down the winding hallways, no one paid him any mind. He was almost to the men's changing rooms, and no one had noticed his hands yet.

It looked like it actually would be as easy as putting his hands in his pockets!

That was until a feminine voice called his name from several feet behind him. He turned around nervously to meet the gaze of one Dr. Ritsuko Akagi. She had a friendly expression on her face but he could tell she was tired by the dark rings under her eyes.

Shinji didn't know what to make of the bottle blond. Most of the time she was cold and calculated, other times she was quite friendly and joked around with Misato. And during his first week living in the city she treated him as if he were made of glass, but at the same time performed many tests on the boy.

She had said that it was standard procedure but he hadn't repeated any tests like the previous ones after that. A routine check-up here and there, synch tests, and simulator training were all the kinds of tests he underwent at NERV now. But in that week Ritsuko had tested his five senses, muscle strength and mass, intelligence, and bodily fluids.

Handing her the urine sample in his provided cup was the most embarrassing thing Shinji had ever done.

Despite her strange nature, Shinji found he liked the faux blond. He was also grateful that unlike his guardian, Dr. Akagi didn't tease him mercilessly. When she had told the lad he would have to provide a urine sample Misato couldn't hold in her giggles. That act had gotten her kicked out of the lab until Ritsuko and Shinji finished their tests.

Even though she had been nothing but nice to him, she still intimidated him. The way she looked at him sometimes reminded him of someone who was seeing something they thought they'd never see again.

"Hello, Dr. A-akagi." Shinji stammered.

"Hello, Shinji. How are your hands today?" Ritsuko asked.

' _Shit! Right to the point, huh doc.'_ Shinji mentally cursed.

He tried to formulate a response but no words came out of his mouth. He had the doctor right where he wanted her, but fear of what might happen to him held his tongue. Ritsuko noticed his panicked expression and commented on it.

"Shinji are you alright?" She asked, concerned.

Shinji took a second to compose himself before he gave a very unsteady "No".

Ritsuko's expression softened. "What's wrong?" She questioned. He lowered his gaze to the floor before replying.

"Something is wrong with me, I need to show you something after the synch test. I can't say what it is right now. A-and can you make sure we're alone in the lab after the test, I don't want Misato to see. I'm sorry for the trouble" He answered.

"It's quite alright, we can't have anything happen you. I'll tell Misato I've scheduled a check-up for you right after the synch test. Now run along and get changed into your new plug suit, the test will begin when you reach the simulation body." Ritsuko instructed.

The Third Child nodded and gave a soft "Thank you" before hurrying down the hallway and into the changing room.

' _I hope he's not going to confess his undying love for me or something. One Ikari trying get into my pants is bad enough'_ Ritsuko thought with a sigh.

Truth be told, Ritsuko did not want to think about the Commander right now. Her feelings for the elder Ikari were muddled at the moment because of his actions during their last lovemaking session. She didn't mind him being rough but when he had called her Yui as he came all over her, she felt truly beyond disgusted.

The worst part was that that she didn't know who felt more disgusted at, him or herself.

She shook her head and banished the awful thoughts from her mind. Then the mask of indifference slipped right back into place. Everyone regarded her as the emotionless chief scientist, so she had to look the part.

All the others kept their distance from her as she walked to the Pribnow Box to monitor the test with Misato and the Bridge Bunnies.

It was not until she rounded the corner of the hallway did Shinji fully close the door to the men's changing room. He hated to spy on her, but he had to make sure she was gone before he started changing. He had to make sure there was absolutely no chance she saw his hands before he was ready to show her.

It also gave him a few seconds to memorize her scent. She smelled of cigarette smoke, LCL, and cats oddly enough. Or at least he thought it was cats. He passed a stray cat on his sprint to the train station and it smelled almost identical. The LCL was easy to pick up on. It was the same stench as blood, and the entire base reeked of it.

Shinji flooded the trivial matters from his mind and changed into his new plug suit as fast as he could. Having an enhanced sense of smell meant he could smell things that he couldn't before, and being in the men's locker room meant he was smelling things he never wanted to smell!

He pressed the button that pressurized his suit and swiftly left the locker room.

When Shinji stepped into the hallway he stopped dead in his tracks. Another smell. But somehow this new odor smelled WRONG. This new stench seemed to set off alarm bells inside Shinji's head. He could detect LCL mixed in with the new scent, but the new smell overpowered it by a lot.

When the door to the women's changing room opened and his fellow pilot Rei Ayanami stepped out, Shinji nearly popped his claws.

The smell was coming from her of all things!

He stood frozen in place as she glanced towards him. She blinked and without a word started off down the hall to the test. She had gotten ten feet away before asking him a question.

"Are you coming, Ikari-kun? The test is about to begin." She informed without looking his way.

"Y-yeah, I'll be there in just a second Ayanami-san." He replied.

She nodded and resumed walking towards the simulation bodies. After she turned the corner Shinji let out the breath he didn't realise he was holding in.

Now the Third Child was really puzzled. Rei Ayanami, the most harmless person he knew, was now somehow setting off mental alarms like she was an angel or something! Her mere presence now screamed danger. But that was ridiculous, it was just Rei. She wasn't anything to be afraid of.

As much as he didn't like it, he was going to trust his instincts for now.

He waited a good 30 seconds before heading for the simulation bodies himself. When he arrived the technicians were preparing the test. Rei was already inside her simulation plug. He mirrored her actions and climbed into his own simulation plug.

Shinji punched a few buttons on the grips in his plug and opened a channel to the Pribnow Box.

He was greeted by Misato, Dr. Akagi, and the only other three adults Shinji trusted, the Bridge Bunnies! The trio consisting of Lieutenants Makoto Hyuga, Shigeru Aoba, and Maya Ibuki were in charge of working with the MAGI and Eva testing, so he saw them often. They were a friendly bunch, especially Maya.

Unlike the other people that worked at NERV they were actually nice to him, took the time to talk to him, and didn't look at him like he was a wild animal. The Bridge Bunnies didn't sit idly by like others, they saw him as a person and not just a pilot. They also appreciated what Shinji put on the line for them, and they let the teen know it.

Makoto was the hopeless romantic of the bunch, always trying to impress Misato. Shigeru was the musician of the group, always talking about how he hoped to play guitar well enough to be in a band one day. And Maya was the heart of the group who Shinji knew better than the men.

Shinji liked Maya because she was quite similar to himself.

Maya hated violence and was soft spoken like Shinji himself was. The mousy technician had become fast friends with the lad due to their similar natures. Over time she got more comfortable around him and vice versa because she was Ritsuko's assistant, and Shinji often spent a lot of time near the good doctor whenever he came into the base. When she had began to open to the boy and told him about her crush on Dr. Akagi, Shinji couldn't help but giggle at the flustered tech at the time.

If her crush were anymore obvious she might as well wear a sign.

Maya turned the tables on him by asking him who he had a crush on. That had gotten the blood flowing into his face. Shinji also liked the fact that Maya knew when to stop her teasing, unlike a certain purple haired captain.

Shinji suppressed a laugh at the memory and continued his small talk with the Bridge Bunnies.

It wasn't long until Ritsuko gave the order for them to cut the chatter and the synch test began in full. It was two long hours of boring concentration but Shinji endured it like a trooper. He focused as hard as he could but the day's events were starting to break him. Ritsuko had repeatedly told him focus during his time in the simulation body.

When the test concluded, Shinji kept his distance from Rei and walked into the Pribnow Box for his results. Shinji smelled her before she entered the room behind him. The Bridge Bunnies paid them no attention as they busily poured over data from the test.

Ritsuko ushered the pilots over to her to give them their results. Their plugsuits made squishing noises with every step they took towards the doctor. Dr. Akagi pointed to her laptop screen before she spoke.

"Rei, you did very well today. Shinji, you were under your normal rate. I expect better next time." Ritsuko lectured.

The pilots gave a soft "Yes ma'am" before waiting to be dismissed. Misato sat sleeping in a chair to their left, snoring softly with a trickle of drool going down her chin. The good doctor kicked her leg lightly and she bolted awake.

"Huh, what!? I'm up!" Misato exclaimed in surprise while wiping the spit from her chin.

"Don't you have some paperwork to do or something? If I'm not allowed to sleep on the job neither are you! The test is over. Why don't you go do something productive while I give Shinji his check-up." Ritsuko sassed.

She turned to the pilots and promptly dismissed them.

"I'll be in my office when you're done Shinji-kun." Misato called sleepily.

"Ok." He replied

He then set off towards the changing rooms, careful to avoid Rei.

He speedily removed his plugsuit and showered before putting on his clothes and heading to Ritsuko's lab.

When he arrived, not a soul was inside the lab so he sat in an empty seat and waited for Ritsuko to teen found he now liked her lab even less than he used to. The sterile smell littered with chemicals was enhanced, and it was not something he liked at all. He was just glad it didn't give him a headache.

A whiff of cigarette smoke from the other side of the door signaled Ritsuko's arrival before she opened the door.

The door was then opened and closed as Dr. Akagi walked into her lab. The nervous boy stood up from his chair faced the doctor. "Alright Shinji what's wrong?" Ritsuko asked. Shinji said nothing in return, he simply held up his healed hands. The good doctor stared in shock at the hands which were supposed to have third degree burns.

"Impossible…" She breathed while taking the boy's hands into her own.

"I noticed it when I woke up this morning." Shinji began.

"You should've come to see me earlier Shinji. This is...I'll have to take some blood from you, but if this is what I think it is…" She trailed off.

"What is it, Doctor Akagi? What's wrong with me?" Shinji pleaded.

"I don't know yet. But I'm going to find out. Have you told anyone about this." Ritsuko asked the scared teen.

"No. But it's not just my hands, there's more." Shinji admitted.

"Oh shit…" She blurted.

Before the boy could show her anything else, Ritsuko rushed to the door and locked it before speeding over to the switch that closed the lab window's shutters and pressed it. The shutters came down over the windows allowing no one to see inside the lab. Ritsuko then walked back over the boy and asked him to continue.

"Well, my sense of smell has been enhanced or something." Shinji continued.

"Enhanced?" The doctor asked.

"It's like I'm part bloodhound or something. I can smell things I couldn't before. I can also follow them, like they leave trails or tracks." Shinji clarified.

Shinji gulped before he spoke. "There's one last thing."

"Go on." Ritsuko encouraged.

"There was this awful pain in my arms today. It felt like my arms were melting. When it got so bad I couldn't take it anymore, this happened…" Shinji explained.

He took a few steps back before giving the doctor a fearful look and popping his claws. Ritsuko squeaked in surprise before hesitantly walking over to the boy and looking closer at the strange looking claws.

"Is it angel contamination?" Shinji fearfully asked.

"Only one way to find out." Ritsuko declared.

She then walked over to one of her lab stations, slipped on surgical gloves, and picked up a clean syringe with a needle. Shinji retracted his claws and stuck out his arm for her. Ritsuko was shocked to see the skin of Shinji's knuckle quickly regenerate the wounds caused by the claws. She shook her head in disbelief and drew the Third Child's blood into the syringe.

She took the blood to the far end of the lab and placed the syringe into a machine that was connected to a computer. Shinji followed to her the far end of the lab and watched her with hopeful curiosity. Ritsuko saw the look on his face and clarified what the machine did.

"This machine was built to specifically test blood for angelic contamination. It's outdated now. The Eva's systems are equipped with better versions of essentially the same design. But using those isn't an option anymore. If this is what I think it is, we'll want this to be kept quiet." The good doctor explained.

There was a ding and the syringe that had been inserted was ejected and the screen of the computer lit up and began to show how much progress the machine had made at deciphering the sample. Ritsuko promptly took the syringe and disposed of it accordingly into the biological material bin. She kept her gloves on for the moment.

The two stared at the screen and waited for the machine to finish analysing Shinji's blood. After nearly a minute, the device had finished its job. Shinji read the screen and was horrified with the results. The screen read 'No Angelic Contamination Detected'.

"What the hell does that mean!?" Shinji yelled. If it wasn't contamination, what else could it be?

Ritsuko removed her gloves and threw them away before grabbing his shoulders in a calming manner. "It means you are a VERY special individual Shinji. You're a mutant, the first born in 20 years." Ritsuko explained.

Shinji's jaw dropped at hearing that. He thought it would be angelic contamination for sure. The stress of the day had finally caught up with him and he collapsed into a chair. Ritsuko pulled up another chair next to his.

"A mutant? You mean like the X-Men?" Shinji asked.

"That's right. You're like them, you're just like Wolverine actually. When I saw your x-rays, I thought it might be possible for you to be a mutant but I wasn't sure." Dr. Akagi nodded.

"But Wolverine's claws are meta, and how do I have the same power as him? Wait a second...YOU KNEW ABOUT THIS!?" Shinji bellowed.

"Yes, but I wasn't sure if it was a mutation at the time. Second Impact unleashed a lot of radiation that caused tons of minor birth defects. As for you having the same mutation as the Wolverine, I have no clue. The only thing that I could find is a theory proposed by X-Men member, Jean Grey before she died." Ritsuko answered.

The theory she spoke of was brainchild of Dr. Jean Grey who, aside from being a member of the X-Men, was also a brilliant mind. She theorised that some mutants may have the same powers as others based on the idea that almost all telepaths shared the power to read minds.

All the droning his teacher did about the X-Men and mutants suddenly came in handy.

In the years before WWII a spike of mutant births had occurred. Many of the mutants that grew up during that time had the unfortunate fate of crossing paths with German forces. One such mutant was Erik Lehnsherr. He and his family were imprisoned at the Auschwitz concentration camp. His parents were killed and he was experimented on until he learned to control his mutant powers.

On the other side of the world, a young telepath named Charles Xavier met the shapeshifting girl named Raven Darkholme. The two then became close friends and went to Oxford together.

Because of the trouble caused by the Hellfire Club, mutants that were attempting to start a nuclear, the CIA put together their own team of mutants to stop them. This team was dubbed the X-Men. Charles Xavier, Erik Lehnsherr, and Raven Darkholme were all originally part of the X-Men.

During the X-Men's final showdown with the Hellfire Club, Erik was corrupted into killing its leader and his former torturer Sebastian Shaw. During the ensuing battle Charles Xavier was crippled and Erik under the new guise of Magneto created the Brotherhood of mutants alongside Raven under the new name Mystique.

With the mutants that remained by his side Charles formed the Xavier's School for Gifted Youngsters. The Brotherhood of Mutants was not heard from for quite some time after that. They reappeared in 1989 in full force by attempting to use the Statue of Liberty as a glorified mutant lightning rod. The Brotherhood once again reappeared in 1991 and caused mass chaos and destruction in San Francisco.

Luckily the X-Men were able to defeat them once more.

The Brotherhood was captured and swiftly executed by the American government. It was then decided by the UN to undergo Operation 'No More Mutants'. The operation consisted of gene therapy pills that prevented mutant genes from surfacing in future generations. The pills were massed produced and shipped to every corner of the planet.

With the amount of civil unrest towards mutants at the time, the majority of the planet's population took the pills without hesitation. By 1995, there were no more recorded mutant births. And later that year an unknown psychic phenomenon killed the entirety of the Xavier School for Gifted Youngsters. The students and X-Men were confirmed dead. Wolverine and Professor Xavier's bodies were never located.

Groups of mutant rebellions popped up in the late 90s here and there but they always lost in the end.

When Second Impact killed half the world's population, it was confirmed that a lot of the casualties were in fact mutants. Fast forward to the present, the only mutant activity in a country not starved for help was sitting in Ritsuko's office.

Shinji was terrified but fascinated with his new abilities. He looked at Ritsuko.

"I suppose this means you're gonna tell my father about this, huh?" He asked.

"ABSOLUTELY NOT! The Commanders cannot know about this! Don't tell anyone about your abilities, who knows what might happen!" Ritsuko shrieked. And she meant what she said. She didn't know what the Commander and the council would do if they found out the Third Child was a mutant.

Shinj's face lit up like a christmas tree when she said.

"You mean it?" Shinji beamed.

"I sure do." Ritsuko confirmed. She glanced at her watch.

"Any longer and Misato will start to suspect something's up. Head on home for tonight, we'll test your abilities another time. If your body does anything else strange, call me." Ritsuko ordered while ushering the boy towards the door.

Shinji gave the doctor a deep bow before stepping into the hallway and thanking her once again. Ritsuko waved to the teen and watched him walk towards Misato's office. She decided right then and there which Ikari's side she was on, and it sure as hell wasn't Gendo's. She had been only a child when mutants died off, but Ritsuko remembered them vividly.

 **XXXXXX**

 **Timeskip- 2 weeks after Shinji's mutant awakening**

It was 12:30 A.M., now officially Friday morning and Shinji had school in a couple of hours. But he couldn't care less, the only class he was doing any good in anyway was English class ironically. He lay there in his bed listening to music, doing his new favorite stress reliever.

Popping and retracting his claws.

He found it very relaxing but he could only do it when no one was around, so he settled for his old stress reliever of clenching and unclenching his fists when people were around. And in the two weeks since his mutant powers surfaced he needed it.

During the first week he and Misato had to take down a rampaging mecha and Ritsuko had riddled him with tests this on his mutant abilities this week. As much work as they were, Shinji was glad the chief scientist had set them up for him.

After only a few days, Shinji could now find his way around using only his nose if he had to, he got stronger, faster, and even a little smarter. As for his claws, well...his claws could stab through kevlar if he applied enough force.

Shinji yawned before taking out his earbuds and closing his eyes. As he drifted off into slumber he had one last conscious thought.

' _What was it Misato said about meeting a new pilot this weekend? I can't remember. Oh well, I'm sure they'll be nice…'_

 **XXXXXX**

 **Well here it is ladies and gentlemen! Ever since I saw Logan I knew I had to do a crossover. I apologise for the lack of new chapters of Endure and Survive. That story takes a lot more of my creative freedom away since it doesn't have the crazy things a story like this does, thus making it far harder to write. But yeah, definitely expect more of this for sure. And I will get back to Endure and Survive sometime. Constructive criticism is always welcome, reviews too.**

 **Sayonara, Peace!**


End file.
